Apparatus and method for scanning a surface

ABSTRACT

Apparatus and method for scanning a surface. An optical system generates a light beam to illuminate a surface. A carrier supports the surface for reciprocating motion with respect to the light beam to form one axis of a raster. A propulsion system moves the carrier at a substantially constant speed and a position sensor provides an output signal representing the surface position with respect to the light beam. A control system responsive to the output signal modulates a sample period reciprocally to carrier speed to achieve substantially constant scan length per sample and to control data acquisition timing.

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application is a continuation of application Ser. No.10/124,138 titled “Apparatus And Method For Scanning A Surface” bySadler et al., filed Apr. 16, 2002, which is a continuation ofapplication Ser. No. 09/317,654, which is a continuing prosecutionapplication of the application under the same Serial No. filed May 24,1999. Priority is hereby claimed from the foregoing applications whichare also incorporated herein by reference.

BACKGROUND OF THE INVENTION

[0002] This invention relates to scanning a surface and moreparticularly to such a system which can achieve constant scan length perdata sample.

[0003] Scanning imaging systems form a map of some characteristic of asurface of interest by exposing the surface to light and measuring aresponse from the surface. A focused beam of light is moved in adeliberate and repeatable pattern with respect to the surface. Theresponse is generally time-correlated to the position of the scanningbeam in order to form a final map of the property with respect to alocation on the surface. In most situations, it is important to be ableto infer the position of the surface represented by each pixel and to beable to guarantee that the pixel spacing is uniform within sometolerance dictated by the size of the features being scanned.

[0004] Relative motion between the light beam and the surface can beachieved by maintaining the surface stationary and moving the beam or,alternatively, keeping the beam stationary while moving the surface. Ahigh performance (high numerical aperture) optical system of reasonablecost, often has a scanner in which a surface moves while theilluminating beam stays in a constant position relative to the beamoptics. Such an arrangement results in the desirable property of highnumerical aperture. Alternatively, the surface may remain fixed with thelight beam being moved. The components that position the surfacerelative to the beam generally exhibit some systematic position errorsthat are a function of position or time. These errors degrade thequality of the final map of the desired property with respect to alocation on the surface.

[0005] The present invention has particular application to gene chipswhich contain arrays of short DNA chains in an array of sequences boundto a substrate (usually glass). The chip is indexed so that theparticular DNA sequence bound in any area is known. A region having ahomogeneous composition is referred to as a “feature.” The DNA chips canbe incubated with a solution containing RNA or DNA bound to afluorescent tag, allowing the binding of RNA to individual features.Such systems can be used for the determination of both genotype and geneexpression levels.

[0006] If fluorescence is observed in a particular region, binding hasoccurred and a DNA sequence is identified by consulting the index of DNApositions on the chip. The present invention is particularly useful inthis context. As will be discussed below, the present invention setsforth a methodology for measuring and compensating position errors whichmay be a function of position or time to an arbitrary level oflinearity.

SUMMARY OF THE INVENTION

[0007] In one aspect, the apparatus for scanning a surface includes anoptical system to generate a light beam and to deliver the beam to asurface. A carrier supports the surface and is mounted for reciprocatingmotion with respect to the light beam to form one axis of a raster. Ofcourse, the surface may be fixed fith the optics arranged to sweep thelight beam. A propulsion system generates forces for moving the carrierand a position sensor generates an output signal representing thesurface position with respect to the light beam. A servo systemresponsive to the output signal is provided for commanding thepropulsion system to move the carrier at a substantially constant speedin a scanning region. A control system responsive to the output signalis provided to modulate a sample period reciprocally to carrier speed toachieve substantially constant scan length per sample and to controldata acquisition timing.

[0008] In one embodiment, the position sensor, which is monotonic andrepeatable, is selected from a group including a counting positionencoder, optical encoder, magnetic encoder, capacitive encoder, laserinterferometer, an LVDT or reflected optical triangulation device. Thepropulsion system may include a motor, voice coil, a galvanometer, a gasjet or a graphite piston in a glass cylinder powered by a gas or liquid.A state observer may be provided to generate an estimate of carrierspeed for use by the sample period modulation system. A system may alsobe provided for compensating for variable integral illumination persample. One such technique includes scaling the amplitude of a measuredsignal by a function of a ratio of an actual sample period to a nominalsample period.

[0009] In yet another embodiment of the invention, data acquisitiontiming is controlled by a state machine that triggers data acquisitionwhen a selected number of new counts in a correct direction hasoccurred. The inputs to the state machine may be quadrature decodeddirection and quadrature decoded count information. The state machine isprogrammed so that new counts in the correct direction are detected bycounting backwards quadrature state changes and incrementing a triggercounter on quadrature state changes only when a backwards counter iszero.

[0010] In yet another embodiment, data acquisition timing is triggeredby the first equivalence of an actual position value and a selectedtrigger position in which a counter is rapidly incremented, for example,ten times.

[0011] The approach of the present invention permits a highly linearscan (in the sense that the servo system actively regulates the sampleperiod to give constant pixel size) even in the presence of disturbancessuch as friction and vibration.

BRIEF DESCRIPTION OF THE DRAWING

[0012]FIG. 1 is a schematic view of the system of the invention.

DESCRIPTION OF THE PREFERRED EMBODIMENT

[0013] With reference to FIG. 1 a “gene chip” or plate 10 is mounted ona carrier 12. The plate 10 includes an array 14 of biochemical specimensor test spots on its surface. The biochemical specimens may be DNAchains bound to the plate 10 which may be glass. Of course, the scanningsystem of the invention has application to scanning systems apart fromscanning gene chips.

[0014] The carrier 12 preferably has a low mass and is mounted forreciprocating movement with respect to a support 16. The carrier 12 andthe support 16 may form an air bearing allowing low friction motion ofthe carrier 12 with respect to the support 16. In the embodimentillustrated in FIG. 1, the carrier 12 is moved by a motor 18 such as alinear motor having one portion fixed on the support 16 and the otherportion on the carrier 12. Alternatively, the carrier 12 may be movedrelative to the support 16 with voice coils, galvanometers, gas jets orgraphite pistons in glass cylinders. Obviously one could move the lenswhile holding the substrate carrier fixed.

[0015] The position of the carrier 12 with respect to the underlyingsupport 16 (and also with respect to a collimated light beam describedbelow) is measured by an encoder 20. It is preferred that the encoder 20be a non-contact position sensing device (in order to reduce friction)to measure position of the carrier 12 with respect to the support 16 asthe carrier 12 moves. Example non-contact sensors include optical,magnetic, or capacitive encoders, laser interferometers, LVDT's orreflective optical triangulation. Counting position encoders such asoptical and non-optical grating encoders allow a particularly simpleimplementation. As another example, one could measure the position of alaser spot on the chip carrier with a CCD wherein the laser projects aline at an angle to the axis of motion.

[0016] An output of the encoder 20 becomes an input to a servo system 22whose output controls the motor 18. The servo system 22 commands themotor 18 to drive the carrier 12 in a reciprocating motion and tomaintain a substantially constant speed in a scanning region to bedescribed hereinbelow.

[0017] A laser 24 and lens 26 form an exemplary optical system fordelivering a focused beam of light onto the gene chip or plate 10. Atest spot within the array 14 may fluoresce upon illumination by thefocused beam and the fluorescence is detected by a detector 28. A sampleperiod modulation system 30 responds to the speed of the carrier 12 toalter the scanner sample period reciprocally to the speed of the carrier12 to achieve a constant scan length per sample and to control dataacquisition timing. The output of the detector 20 is then stored instorage element 32 which may be part of a digital computer system (notshown). The sample period modulation system 30, such as a digitalintegrator, responds to position information from the encoder 20. Thesystem 30, in some circumstances, may derive carrier 12 speed bymeasuring the time interval between sensed position increments from theencoder 20. Alternatively, a state observer 34 may be provided whichincludes a dynamic model of the carrier-motor-encoder system. The stateobserver 34 responds to an output from the encoder 20 and to commands tothe motor 18 from the servo system 22 to provide an estimate of a statevariable such as speed of the carrier 12. This speed is used by thesample period modulation system 30 to modulate the scanner sample periodto achieve substantially constant scan length per sample.

[0018] In operation, the carrier 12 reciprocates rapidly under thefocused light beam from the laser 24. The servo system 22 attempts tomaintain a highly constant speed of the carrier 12 in the scanningregion, but speed can vary because of disturbances such as friction andvibration. Because speed may vary, actual speed is measured, inferred orestimated and any speed variation serves as an error signal formodulating the sample time period in the system 30. That is, if thespeed is too low then the sample period will be increased to assure aconstant scan length per sample. Similarly, if the speed of the carrier12 is too high, the sample period will be reduced to achieve constantscan length per sample. Speed errors can thereby be compensated to anarbitrary level of linearity. Said another way, T_(SN)−T_(S(N−1))−kEwhere T_(SN) is the sample period for sample N, T_(S(N−1)) is the sampleperiod for the sample N−1, and E is the variation or error in speedwhich, of course, may be a positive or negative value. It is recognizedthat there is a trade-off in the uniformity of illumination per unitdistance as more nearly constant scan length is achieved.

[0019] In a particularly simple implementation of the system of theinvention, the encoder system 20 is used to control scan speed only to alevel at which spatial variations of saturation and/or bleaching of dyemolecules in the array 14 are kept below an acceptable limit. Pixelacquisition is then simply synchronized to (triggered by) the encoder 22output directly and the number of samples averaged within a pixel iskept fixed at a number that can be completed in the shortest expectedpixel time.

[0020] For realistic conditions, the small gaps in data acquisition willbe sufficiently averaged over by the reading spot size being wider thanthe gaps. A synchronization signal can be derived directly fromtransitions of a grating encoder (in which case it can be set to onevalue out of a fixed (infinite) set of ratios relative to the gratingperiod) or it can be derived from the digitized encoder outputs, oftenallowing further interpolation. For example, with a nominal linear scanspeed of lm/s, a pixel size of 10 μm and a gap of 1 μm (which doeshardly degrade S/N for a 5 μm FWHM spot) a speed variation of 10% wouldbe acceptable if other sources are neglected. Spending half of thismargin on, for example, clock frequency drift of the oscillatorcontrolling sample acquisition still allows for a 5% P-V speedvariation. (In a typical system, 226 samples would be acquired in 9 μsat a fixed rate of one sample/40 ns). Alternately, one can accumulate asmany pixels as possible during the pixel time and then normalize byeither dividing by the number samples (times a scale factor) or by usinga look-up table for speeding up this division.

[0021] As stated above, modulating the sample period according to theinvention to deliver constant pixel size results in variable integralillumination per sample. This effect can be compensated for by scalingthe amplitude of the measured signal by a function of the ratio of theactual sample period to a nominal value. In the case of laser excitedfluorescent scanning, the function will be proportional to thereciprocal of the sample period only if the fluorescent dye is in itslinear region, that is, not saturated or bleaching appreciably.Alternatively, variable integral illumination per sample can becompensated by controlling intensity of the light source. Note that anyrepeatable and invertible relationship between integral illumination andemission intensity can be used for the basis for a compensating functionin the non-linear case. The scaling operation changes noiseproportionally to amplitude rather than to the square root of amplitudeso that artifacts of the compensation may be noticeable.

[0022] In a particularly preferred embodiment, the position sensor orencoder 20 triggers data acquisition at specified positions or positionintervals. The sensor output signal is integrated using a digitalintegrator which may be included in the sample period modulation unit 30that accumulates signal samples at, for example, a 40 ns rate. Thenumber of samples varies with the velocity of the carrier 12. The dataread includes the integrated signal and number of samples (integrationtime). It is appropriate to use 32 bits, 10 bits for the number ofsamples and 22 bits for the signal. The signal value is divided by aquantity which is the number of samples divided by a scale factor. Thesensed position is compared to a sequence of trigger positions. Thiscomparison is based on a threshold and requires hysteresis (where theoutput depends on the input and its recent history) to prevent multipletriggers for the same pixel. Defining the amount of hysteresis to use isan issue. If the position sensor were ideal and the motion were alwaysin the direction of scan travel, then no hysteresis is needed. Realsystems, however, have vibration and sensor jitter (position thatalternates between two values due to the least significant bit'sthreshold).

[0023] Hysteresis defines separate thresholds for high to low and low tohigh input transitions. We want the output to ignore the input after thethreshold is crossed the first time. We also need to be able to changethe direction and change the threshold (trigger position).

[0024] The position sensor jitter will result in extra pixels beingacquired. One solution to this situation is to implement a state machinethat triggers data acquisition when the desired number of new counts inthe correct direction has occurred. The servo system defines the correctdirection for this state machine. Other state machine inputs are thequadrature decoded direction and the quadrature decoded count (thatindicates when a quadrature state change occurs). With a 1 μm encoderresolution and a 10 μm pixel size, data acquisition is triggered every10 new encoder counts. New counts in the correct direction are detectedby counting backwards quadrature state changes and incrementing atrigger counter on quadrature state changes only when the backwardscounter is zero (no backwards state changes have been recorded).

[0025] Another way of implementing this scheme is to compare the actualposition value to a trigger position and on the first equivalencetrigger data acquisition and add 10 to the trigger position. The triggerposition can be implemented as a counter that is rapidly incremented 10times. Ideally, this counter increment occurs before the next encoder(actual position) state change, which is about one microsecond in oursystem, so the counter must be incremented at a 100 ns (10 mhz) rate.

[0026] Note that the encoder triggered data acquisition is registered byan index pulse at each end of a scan line. This index signal is alsoderived from the sensed position and is also susceptible to multipletransitions unless hysteresis is used. The same position qualificationscheme used for the data trigger can be used for the two indices.

[0027] Velocity controlled sampling avoids this position comparison. Itrequires predicting the sample time. The digital integrator must now betold how many samples to take by the servo because the servo and digitalintegrator are asynchronous and the servo is slower. The prediction isstill limited by position sensor jitter if the velocity is derived fromthe position rather than directly measured. The servo loop runs at 100microseconds but the data acquisition must run at 10 microseconds (for10 μm pixels).

[0028] It is intended that all modification and variations of theinvention disclosed herein be included within the scope of the appendedclaims.

What is claimed is:
 1. A method for scanning a surface comprising:generating a light beam and delivering the beam to a surface; detectinga response of the surface to the light beam; moving the light beam andsurface with respect to one another at a relative speed; wherein a voicecoil provides the reciprocating.
 2. A method according to claim 1wherein the moving comprises a reciprocating.
 3. A method according toclaim 2 wherein the relative speed is lm/s.
 4. A method according toclaim 2 wherein the reciprocating provided by the voice coil occursalong one axis of a raster.
 5. A method according to claim 2 wherein thereciprocating takes place under a focused light beam.
 6. A methodaccording to claim 2 wherein the surface is a surface of an array ofbiochemicals.
 7. A method according to claim 6 wherein the array ofchemicals is a DNA chip.
 8. A method according to claim 6 wherein thereciprocating is provided by the voice coil which is coupled between acarrier holding the array and a support.
 9. A method according to claim6 wherein the reciprocating is provided by the voice coil which iscoupled to move a lens through which the light beam is delivered.
 10. Amethod according to claim 2 additionally comprising compensating forvariable integral illumination per sample.
 11. The method of claim 10wherein the compensating comprises scaling amplitude of a measuredsignal by function of the ratio of an actual sample period to a nominalsample period.
 12. A method for scanning a surface comprising:generating a light beam and delivering the beam to a surface of an arrayof chemicals; detecting a response of the surface to the light beam;reciprocating the light beam and surface with respect to one another ata relative speed; and compensating for variable integral illuminationper detected data sample of the response. wherein a voice coil providesthe reciprocating.
 13. An apparatus for scanning a surface of a chemicalarray comprising: a detector for detecting an optical signal from thesurface; a carrier to support the surface, wherein the detector or thecarrier moves with respect to the other; a voice coil to cause themoving of the detector or carrier with respect to the other.
 14. Anapparatus according to claim 13 wherein the voice coil is connected tomove the detector.
 15. An apparatus according to claim 13 wherein thevoice coil is connected to move the carrier.
 16. An apparatus accordingto claim 13 additionally comprising an optical system to generate alight beam and to deliver the beam to the surface.
 17. An apparatusaccording to claim 16 wherein the optical system includes a lens throughwhich the light beam is delivered to the surface.
 18. An apparatusaccording to claim 16 wherein the voice coil is connected to move thelens.
 19. An apparatus according to claim 13 wherein the voice coilmoves the detector or the carrier moves with respect to the other at aspeed of lm/s.
 20. An apparatus according to claim 13 wherein themovement provided by the voice coil comprises a reciprocating movementwhich occurs along one axis of a raster.
 21. An apparatus according toclaim 17 wherein the optical system delivers a focused light beam to thesurface.